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Graduate student instructor (GSI). University of California, Berkeley Dynamic modeling of biological systems. Upper division course in systems biology. Covers dynamic modelling using Berkeley Madonna differential equation solver. Evolutionary genetics. : Taught
evolutionary and population genetics at upper-division
undergraduate level.
Guest lecturer. Santa Fe Institute . Presented
tutorial sessions to Swarm, the
simulation framework, to students at SFI's annual “Complex
Systems” and “Economics” Summer Schools.
Sessions ranged from two-hour sessions to full day tutorials.
Presented an afternoon tutorial session at Artificial Life VI in
June 1998. Physics Tutor. School of Physics, University
of Sydney .
In this role I taught Physics to undergraduates as well as
marking exams and assessing laboratory work. I wrote Pascal
programs on PCs to demonstrate interactive physics problems such
as chaotic, quantum mechanical and astrophysical
applications.
Journal papers[Cao:etal:2004] K. Cao, A.M. Moormann, K.E. Lyke, C. Masaberg, O.P. Sumba, O.K. Doumbo, D. Koech, A. Lancaster, M. Nelson, D. Meyer, R. Single, R.J. Hartzman, C.V. Plowe, J. Kazura, D.L. Mann, M.B. Sztein, G. Thomson, and M.A. Fernandez-Vina. 2004. “Differentiation between African
populations is evidenced by the diversity of alleles and
haplotypes of HLA class I loci”. Tissue Antigens. 4. 293-325. [Williams:etal:2004] F Williams, A Meenagh, R Single, M McNally, P Kelly, M.P Nelson, D. Meyer, A Lancaster, G Thomson, and D Middleton. 2004. “High resolution HLA-DRB1 identification of a caucasian population”. Human Immunology. 1. 66-77. Book chapters[Lancaster:etal:2003b] Alex Lancaster, Mark P Nelson, Richard M Single, Diogo Meyer, and Glenys Thomson. 2003b. Software framework for Biostatistics Core. JA Hansen and B Dupont. in press. HLA 2002: Immunobiology of the Human MHC. IHWG Press. [Meyer:etal:2003] Diogo Meyer, Richard M Single, Steven J. Mack, Alex Lancaster, Mark P Nelson, M. Fernánndez-Viñaa, Henry Erlich, and Glenys Thomson. 2003. Haplotype Frequencies and Linkage Disequilibrium among
classical HLA genes. JA Hansen and B Dupont. in press. HLA 2002: Immunobiology of the Human MHC. IHWG Press. [Single:etal:2003b] RM Single, D Meyer, Steven J. Mack, Alex Lancaster, Mark P Nelson, M. Fernánndez-Viñaa, Henry Erlich, and G Thomson. 2003b. Single locus polymorphism of classical HLA
genes.. JA Hansen and B Dupont. in press. HLA 2002: Immunobiology of the Human MHC. IHWG Press. Peer reviewed conference papers[Lancaster:etal:2003] Alex Lancaster, Mark P. Nelson, Richard M. Single, Diogo Meyer, and Glenys Thomson. 2003. “PyPop: a software framework for population genomics: analyzing
large-scale multi-locus genotype data”. Pacific Symposium on Biocomputing 8. R B Altman. et al.. World Scientific. Other papers, postersA K Lancaster, M P Nelson, D D Meyer, S J Mack, R M Single, J A Hollenbach, and G. Thomson. 2001. “Preliminary population genetic analyses of data from the IHWG anthropology/human genetic diversity component”. 27th Annual Meeting of the American Society for
Histocompatibility and Immunogenetics. San FranciscoCalifornia USA
. October 13-17, 2001. . Human Immunology. S63.
Researcher and software
developer This position consisted of two main consecutive projects: Research programmer for Network Dynamics/Beowulf
project. Primary software developer in a team of 3-4, working on
construction of a 25 node Beowulf cluster, worked
on everything from node assembly to developing parallel
applications. Responsible for software installation script development
(kickstart); RPM packaging; MOSIX (load-balancing software)
installation; NFS, NIS, RAID, PVM, MPI installation and
configuration. Translated/extended a 4000 line C++ framework into
Java. The program was a multithreaded, designed for use
in the cluster
Applications and infrastructure programmer
for the Swarm Program. Part of a team of two software engineers at the Santa Fe
Institute. Swarm is fully object-oriented discrete event
simulation software toolkit for constructing agent-based
simulations of complex phenomenon (molecular and cellular
systems, bacterial colonies, forest ecosystems, the
stockmarket, ancestral publeo villages and factory supply
chains). development of an inter-language layer to allow
Java applications to talk to the Swarm kernel (written largely
in Objective C) using Sun's Java Native Interface (JNI)
core feature development work on the kernel in
Java (JDK 1.2), C and Objective C (including: extensions to
the discrete two-dimensional space library, complete
implementation of object serialization features, and other
core API work).
from-scratch development of numerous Swarm
models in Java and Objective C using the Swarm kernel
and maintenance and extensions of over 20 existing
models
part of the development and maintenance of
complete literate programming system for Swarm using the
DocBook DTD SGML, involving automatic generation of
documentation from Swarm source and complete backend support
for generating Word (RTF), HTML, PostScript and DVI output
using Sun JDK javadoc/doclet customization layer, Emacs Lisp
and various XML and DSSSL tools.
binary packaging of Swarm and other
libraries (hdf5, libffi) for Red Hat Linux using the Red
Hat Package Manager (RPM), and involved in packaging for
Debian Linux, Solaris and Windows 95/98/NT.
primary website developer/maintainer, using
combination of HTML, XML, LaTeX and LaTeX2HTML tools
including a complete XML-based website for the Swarm
Development Group.
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